Contacts of the strand formed by residues 118 - 139 (chain B) in PDB entry 4DEQ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 118 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B GLY* 3.6 0.2 - - - -
68B THR* 2.9 35.2 + - - -
85B TYR* 4.9 0.3 + - - -
109B GLN* 4.2 10.2 - - + +
110B GLY 3.2 28.0 - - - +
111B ASN* 3.5 21.8 - - - +
112B THR* 5.0 4.5 - - + +
116B ASP* 4.1 9.4 - - + +
117B VAL* 1.3 76.2 - - - +
119B VAL* 1.3 71.0 - - - +
120B ALA 4.0 0.2 + - - -
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B MET* 4.2 15.7 - - + -
65B ALA* 3.9 21.3 - - + -
66B VAL 3.4 9.2 - - - +
67B GLY* 4.2 0.2 - - - -
109B GLN 4.9 1.2 - - - +
117B VAL* 4.2 14.3 + - + +
118B VAL* 1.3 84.6 - - - +
120B ALA* 1.3 65.3 + - - +
121B VAL* 4.0 8.8 + - + +
149B TYR* 4.2 21.1 - - + +
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ALA* 3.4 4.9 - - - -
66B VAL* 2.8 28.4 + - + +
85B TYR* 3.4 24.0 - - - +
108B PHE* 3.5 28.0 - - + -
109B GLN 4.1 10.1 - - - +
118B VAL 4.0 0.2 + - - -
119B VAL* 1.3 72.9 - - - +
121B VAL* 1.3 65.1 + - - +
122B PHE* 3.6 6.4 + - - -
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B MET* 4.8 11.9 - - + -
64B THR* 4.1 7.2 - - - +
65B ALA* 3.7 13.7 - - + -
108B PHE* 3.9 8.8 - - - -
119B VAL* 4.0 11.1 + - + +
120B ALA* 1.3 71.8 - - - +
122B PHE* 1.3 77.1 + - - +
123B PRO* 3.9 0.7 - - - +
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Residues in contact with PHE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B VAL* 3.2 47.8 - - + -
64B THR 2.8 19.4 + - - +
65B ALA* 3.8 11.2 - - - -
66B VAL* 3.8 20.4 - - + -
87B ILE* 3.8 26.5 - - + -
89B VAL* 5.2 4.5 - - + -
99B ILE* 3.9 23.6 - - + -
108B PHE* 3.9 11.7 - + - -
120B ALA 3.7 8.3 - - - -
121B VAL* 1.3 86.3 - - - +
123B PRO* 1.3 73.2 - - + +
124B LYS* 3.3 21.5 + - - +
126B LEU* 4.3 8.5 - - + -
131B VAL* 5.4 2.0 - - + -
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Residues in contact with PRO 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ILE* 3.9 17.3 - - + -
100B LYS 3.9 22.2 - - - +
101B GLU* 4.5 19.7 - - + +
106B VAL* 4.0 18.8 - - + -
108B PHE* 4.4 7.2 - - + -
121B VAL 3.9 2.2 - - - +
122B PHE* 1.3 87.2 - - + +
124B LYS* 1.3 65.2 + - + +
126B LEU* 6.3 0.4 - - + -
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Residues in contact with LYS 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LYS 6.0 2.7 - - - +
122B PHE* 3.4 19.5 - - - +
123B PRO* 1.3 83.3 - - + +
125B PRO* 1.3 83.8 - - + +
126B LEU* 3.6 18.1 - - + +
162B SER 4.8 11.2 + - - +
164B SER 4.0 21.6 + - - -
165B PRO* 5.5 1.3 - - - -
166B CYS 5.5 3.2 + - - -
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Residues in contact with PRO 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B PHE* 3.7 26.4 - - + -
63B VAL 3.6 7.2 - - - +
64B THR* 3.9 25.5 - - + -
122B PHE 5.6 0.2 - - - +
124B LYS* 1.3 95.6 - - + +
126B LEU* 1.3 65.1 + - - +
156B TYR* 3.6 21.3 - - + +
160B SER* 5.1 8.7 - - - +
162B SER 4.9 0.5 - - - +
163B GLY* 4.1 10.6 - - - -
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ARG 3.2 2.3 - - - +
62B PHE* 4.3 2.7 - - - -
63B VAL* 2.8 38.8 + - - +
89B VAL* 4.4 7.4 - - + -
99B ILE* 3.7 39.5 - - + -
122B PHE* 4.3 7.9 - - + -
123B PRO* 6.3 0.2 - - + -
124B LYS* 3.6 21.1 - - + +
125B PRO* 1.3 83.4 - - - +
127B ILE* 1.3 62.8 - - - +
128B THR* 3.5 13.9 + - + +
163B GLY 3.4 12.8 - - - +
164B SER 4.0 4.5 - - - +
165B PRO* 3.6 34.5 - - + -
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B LEU* 4.2 26.0 - - + +
61B ARG 3.4 3.6 - - - -
62B PHE* 3.6 36.6 - - + -
91B SER* 5.9 0.7 - - - -
126B LEU* 1.3 67.0 - - - +
128B THR* 1.3 65.9 + - - +
153B ILE* 3.6 28.3 - - + -
163B GLY* 2.9 31.7 + - - +
165B PRO* 4.1 11.4 - - - +
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Residues in contact with THR 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B LEU* 3.9 4.9 - - - +
60B LEU* 3.8 11.2 - - - -
61B ARG* 2.9 27.6 + - - +
63B VAL* 3.6 26.7 - - + -
89B VAL* 3.5 23.4 - - + +
90B SER* 2.6 39.9 + - - -
91B SER* 5.1 1.1 - - - +
126B LEU* 3.8 9.9 - - + +
127B ILE* 1.3 77.9 - - - +
129B ARG* 1.3 59.1 + - - +
130B PHE 3.3 6.9 + - - +
131B VAL* 4.4 2.5 - - + -
165B PRO* 5.4 1.3 - - - -
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Residues in contact with ARG 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLU* 3.8 30.0 + - - +
50A ARG* 4.4 16.9 - - - +
51A GLU* 4.7 6.5 + - - -
56B ASP* 2.8 37.7 + - - +
57B LEU* 2.9 38.9 + - - +
58B GLY* 3.0 29.6 + - - +
59B LEU* 3.4 22.9 - - - +
60B LEU* 3.9 7.7 - - + +
90B SER 3.0 2.6 + - - -
91B SER 3.6 19.2 + - - +
128B THR* 1.3 80.1 + - - +
130B PHE* 1.3 78.8 + - + +
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Residues in contact with PHE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ARG* 4.0 28.3 - - - -
54B GLN* 3.6 23.3 - - - +
55B VAL 3.5 4.7 - - - +
56B ASP* 3.5 37.0 - - + -
89B VAL* 3.5 1.9 - - - -
90B SER* 2.8 35.4 + - - +
91B SER 3.5 6.7 - - - -
92B ASN* 3.4 6.5 - - - -
93B GLY* 3.2 38.4 - - - -
96B TRP* 3.7 19.5 - - + -
128B THR* 3.3 6.9 + - - -
129B ARG* 1.3 95.9 - - + +
131B VAL* 1.3 68.6 + - - +
132B ARG 4.3 0.4 - - - -
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B ILE 4.0 1.2 - - - +
54B GLN* 3.3 3.4 - - - -
55B VAL* 3.1 41.1 + - + +
57B LEU* 4.2 20.9 - - + -
63B VAL* 4.4 19.3 - - + -
66B VAL* 4.5 18.6 - - + -
87B ILE* 4.3 17.7 - - + -
88B ASP 4.0 3.1 - - - -
89B VAL* 4.4 5.4 - - + -
122B PHE* 5.4 1.8 - - + -
128B THR* 4.4 5.4 - - + -
130B PHE* 1.3 81.2 - - - +
132B ARG* 1.3 60.4 + - - +
133B ILE* 4.1 10.0 + - + +
146B PHE* 5.1 2.3 - - + -
148B VAL* 4.7 11.9 - - + -
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Residues in contact with ARG 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B TRP* 3.3 66.0 - - + +
53B ILE 3.6 2.9 - - - -
54B GLN* 3.1 29.0 + - + +
87B ILE* 3.5 5.7 - - - +
88B ASP* 2.9 43.8 + - + +
93B GLY 5.2 0.6 + - - -
96B TRP* 3.4 58.2 - - + +
131B VAL* 1.3 72.4 - - - +
133B ILE* 1.3 62.5 + - - +
134B LYS* 4.0 12.4 + - + +
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Residues in contact with ILE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B TRP* 3.3 7.1 - - - +
53B ILE* 2.8 43.4 + - + +
66B VAL* 4.9 13.5 - - + -
68B THR* 5.5 0.9 - - - +
85B TYR* 3.7 32.3 - - + -
86B LYS 3.9 2.7 - - - -
87B ILE* 4.6 9.6 - - + -
131B VAL* 4.8 8.7 - - + +
132B ARG* 1.3 74.5 - - - +
134B LYS* 1.3 64.4 - - - +
135B PRO* 3.6 2.9 - - - +
144B MET* 3.7 36.8 - - + -
146B PHE* 3.9 34.1 - - + -
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Residues in contact with LYS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B TYR 4.6 8.3 - - - +
50B ARG* 6.1 1.6 - - - +
51B GLU 4.1 4.7 - - - +
52B TRP* 4.2 15.0 - - + -
85B TYR* 3.3 2.6 - - - +
86B LYS* 2.8 65.2 + - + +
88B ASP* 3.2 39.0 + - - +
98B THR* 4.7 5.3 + - - +
132B ARG* 4.4 16.4 - - + +
133B ILE* 1.3 77.6 - - - +
135B PRO* 1.3 68.5 - - - +
136B ALA* 4.5 0.9 - - - +
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Residues in contact with PRO 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B TRP* 4.5 7.2 - - + -
48B SER 5.6 0.2 - - - +
49B TYR* 3.3 29.8 - - - +
51B GLU 3.3 20.6 - - - +
52B TRP* 4.4 1.8 - - - -
82B VAL* 4.0 15.7 - - + -
84B THR 4.1 0.4 - - - +
85B TYR* 3.8 9.4 - - + -
133B ILE* 3.6 9.2 - - + +
134B LYS* 1.3 83.1 - - - +
136B ALA* 1.3 59.4 + - - +
138B TRP* 4.7 3.1 - - + -
142B ILE* 4.1 34.8 - - + -
144B MET* 4.1 21.1 - - - -
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B TYR* 4.4 11.6 - - + +
84B THR* 2.8 28.5 + - - +
85B TYR* 4.2 6.1 - - - -
86B LYS* 5.0 7.4 - - + +
107B LEU* 4.4 17.5 - - + -
134B LYS 3.5 1.5 + - - +
135B PRO* 1.3 73.9 - - - +
137B THR* 1.3 66.8 + - + +
138B TRP* 3.2 16.8 - - - -
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Residues in contact with THR 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B VAL* 3.1 12.6 - - - +
83B LYS* 2.9 38.1 + - - +
84B THR* 2.5 33.8 + - - +
107B LEU* 6.2 1.1 - - + -
136B ALA* 1.3 85.8 - - + +
138B TRP* 1.3 67.2 + - - +
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Residues in contact with TRP 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ASP* 3.2 31.4 + - + +
48B SER* 3.6 35.7 - - - -
49B TYR* 4.1 3.8 - + + -
81B TYR 3.4 14.4 - - - +
82B VAL* 4.1 5.2 - - + -
83B LYS* 3.7 20.0 + - - +
135B PRO* 4.5 4.7 - - + -
136B ALA 3.2 22.4 - - - -
137B THR* 1.3 94.6 - - - +
139B GLU* 1.3 61.0 + - - +
140B THR 4.2 4.0 + - - -
141B GLY* 3.5 35.8 - - - +
142B ILE* 3.6 24.0 - - + -
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Residues in contact with GLU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LYS 4.0 0.2 - - - +
80B TYR* 4.0 0.2 - - - -
81B TYR* 2.9 59.9 + - + +
83B LYS* 4.1 21.4 + - + +
138B TRP* 1.3 71.0 - - - +
140B THR* 1.3 87.0 + - + +
141B GLY 2.6 19.4 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il